MolNFT v1 · #12747 · protein
Formate dehydrogenase N from E. COLI
1KQG · Formate dehydrogenase, nitrate-inducible, major subunit: “Formate dehydrogenase N from E. COLI”. X-ray diffraction, 6 ligands (SF4, MGD, HEM), 15 pockets (best druggability 0.89). MolNFT v1 #12747 on GenesisL1: 3D structure, binding…
- PDB
- 1KQG
- Type
- protein
- Length
- 1,487 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase, nitrate-inducible, major subunit; Formate dehydrogenase…
- EC
- 1.2.1.2
- UniProt
- P24183, P0AAJ3, P24185
- Ligands
- SF4, MGD, HEM, CDL, HQO, 6MO
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase, nitrate-inducible, major subunit (EC 1.2.1.2) | protein | 982 | 31% helix, 19% strand | P24183 |
| B | Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit (EC 1.2.1.2) | protein | 289 | 30% helix, 19% strand | P0AAJ3 |
| C | Formate dehydrogenase, nitrate-inducible, cytochrome B556(FDN) subunit (EC 1.2.1.2) | protein | 216 | 76% helix, 3% strand | P24185 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 5 copies · chains A, B
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C
- CDL · Cardiolipin · ligand · chains B, C
- HQO · 2-heptyl-4-hydroxy quinoline N-oxide · ligand · chains C
- 6MO · Molybdenum(vi) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.89 | 0.96 | 88 | MGD, 6MO |
| 2 | 276 | 0.84 | 0.94 | 37 | HEM |
| 3 | 655 | 0.82 | 0.86 | 65 | HEM, HQO |
| 4 | 925 | 0.75 | 0.78 | 76 | empty |
| 5 | 170 | 0.58 | 0.82 | 39 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2565 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 1944 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P24183
- Every structure of UniProt P0AAJ3
- Every structure of UniProt P24185
- Elsewhere: RCSB PDB 1KQG · PDBe 1KQG · UniProt P24183 · UniProt P0AAJ3 · UniProt P24185
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